Just a wild guess, but the game could be rendering some faces with the hull texture when they should be transparent...? I get this problem sometimes when I'm modding ships. If that's the problem, setting the material ID of the troublesome faces to "hole" in Wings3d or a similar program should resolve it - once designated with the texture "hole", the game will read the distorted faces as invisible.
Again, this is just a guess - sorry if it doesn't help.
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